Sequence data and evidence of possible airborne spread in the 2001 foot‐and‐mouth disease epidemic in the UK

In conclusion, this study provides further data to suggest that full genome sequencing is a powerful tool that can be used to substantiate disease tracing at farm-to-farm level. However, it is important to consider that genome sequences indicate only the genetic relationships of the viruses sampled, and do not on their own provide information regarding the route of transmission between animals or between IPs. Furthermore, the presence of intermediate (and unsampled) infected farms cannot be ruled out for the majority of the transmission events considered in this study. Previous analysis of field data collected during the 2001 FMD epidemic has highlighted the difficulties of determining the precise mechanism by which FMDV entered many of the affected farms. Although it is still difficult to prove the importance of airborne FMDV spread, in this instance, the sequence data are consistent with the hypothesis that IP27 was the source for multiple outbreaks in northern Cumbria. Epidemiological tracing has failed to uncover other plausible mechanisms of transmission for these IPs (Honhold 2006); therefore, the sequence data support the previous study of Gloster and others (2005) that proposed that these farms were infected via the airborne route. In the future, further refinements to the understanding of the variability of FMDV that arises within an infected herd, as well as the mechanisms that drive consensus sequence evolution, will help improve the interpretation of this type of fine-scale molecular epidemiological data.